17-19706752-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099646.3(SLC47A2):c.737G>A(p.Ser246Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000686 in 1,604,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099646.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC47A2 | NM_001099646.3 | c.737G>A | p.Ser246Asn | missense_variant | 9/17 | ENST00000433844.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC47A2 | ENST00000433844.4 | c.737G>A | p.Ser246Asn | missense_variant | 9/17 | 5 | NM_001099646.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239828Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 130346
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1452244Hom.: 0 Cov.: 33 AF XY: 0.00000830 AC XY: 6AN XY: 722726
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.845G>A (p.S282N) alteration is located in exon 9 (coding exon 9) of the SLC47A2 gene. This alteration results from a G to A substitution at nucleotide position 845, causing the serine (S) at amino acid position 282 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at